Import and local transmission analysis

The input for this analysis is the results from the maximum likelihood mapping of the geographical states on the full phylogenetic tree of the 9732 genomes.

Import versus local transmission for Norway, Australia, Europe and the USA

From the mapped geographical lineage distributions we can derive the number of importation and local transmission events for each location (based on the available sequences). NB. we do not account for unobserved infections (sequences), and hence the estimated number only reflects the fraction of sequenced genomes that is assigned to specific lineages. The relative growth between the lineages (growth of an transmission lineage implies local transmission), is an important quantity and tells us how dominant specific lineages have become over time. This too could be affected by nonrandom sampling such as targeted sampling of lineages with anitibiotic resistance.

Cumulative growth of transmission lineages

The following plots show the cumulative number of sequences obtained from each estimated transmission lineage over time

name_date_NOR = name_date[name_date$name%in%nor_tips,]
linfo_NOR = lineage_info(Result_NOR,name_date = name_date_NOR)
LineageHomology::lineage_growth_cumulative(linfo_NOR,datelims=c("2015-01-01","2019-06-15","1 year"))

name_date_AUS = name_date[name_date$name%in%aus_tips,]
linfo_AUS = lineage_info(Result_AUS,name_date = name_date_AUS)
LineageHomology::lineage_growth_cumulative(linfo_AUS,datelims=c("2016-07-01","2018-06-15","5 months"))

name_date_USA = name_date[name_date$name%in%usa_tips,]
linfo_USA = lineage_info(Result_USA,name_date = name_date_USA)
LineageHomology::lineage_growth_cumulative(linfo_USA,datelims=c("2008-07-01","2019-06-15","2 year"))

name_date_EUR = name_date[name_date$name%in%eur_tips,]
linfo_EUR = lineage_info(Result_EUR,name_date = name_date_EUR)
LineageHomology::lineage_growth_cumulative(linfo_EUR,datelims=c("2008-07-01","2019-06-15","2 year"))

Aggregated estimates of import, local transmission and export over the full phylogeny:

c1 = Summarize_import_export_local_transmission(implocexp_NOR); c1
##                                                  2.5%          50%        97.5%
## Import                                    706.8500000  736.0000000  764.0000000
## Local transmission                       1929.4250000 1967.5000000 2004.0500000
## Export                                    922.4750000  980.5000000 1028.0000000
## Import / ( Import + Local transmission )    0.2681245    0.2722397    0.2760066
c2 = Summarize_import_export_local_transmission(implocexp_AUS); c2
##                                                  2.5%          50%        97.5%
## Import                                    356.4750000  371.5000000  391.0000000
## Local transmission                       2152.0000000 2175.0000000 2199.0500000
## Export                                    312.4750000  346.0000000  381.6750000
## Import / ( Import + Local transmission )    0.1421083    0.1458865    0.1509623
c3 = Summarize_import_export_local_transmission(implocexp_USA); c3
##                                                  2.5%          50%        97.5%
## Import                                    370.9500000  390.0000000  407.5750000
## Local transmission                       2574.3750000 2595.5000000 2620.1000000
## Export                                    586.9000000  617.0000000  645.0000000
## Import / ( Import + Local transmission )    0.1259454    0.1306314    0.1346165
c3 = Summarize_import_export_local_transmission(implocexp_EUR); c3
##                                                  2.5%         50%        97.5%
## Import                                   4.494750e+02  476.000000  499.5250000
## Local transmission                       4.233950e+03 4266.500000 4306.0000000
## Export                                   6.200000e+02  643.500000  662.0000000
## Import / ( Import + Local transmission ) 9.597143e-02    0.100369    0.1039481

In Norway we estimate that around 27% of locally observed cases can be attributed due to importation events.
This is more than twice that estimated for the other locations (Australia, the USA, and Europe in general).

Stratifying the estimates on the periods 2010-2014, 2014-2018, and 2010-2018 (total), we obtain the following estimates

By dividing importation and exportation by (import + local transmission) and (export + local transmission), respectively, we obtain the following estimates:

The fraction of total events that are imports, exports and local transmissions in the period 2000-2018 are visualized below.

#pdf("/Users/magnusnygardosnes/Dropbox/10000_Lovers/Junk_used_for_exploratory/Temp/imp_exp_loc_NOR.pdf", width = 10, height = 8)
plot_relative_fraction(implocexp_NOR)

#dev.off()

#pdf("/Users/magnusnygardosnes/Dropbox/10000_Lovers/Junk_used_for_exploratory/Temp/imp_exp_loc_AUS.pdf", width = 10, height = 8)
plot_relative_fraction(implocexp_AUS)

#dev.off()

#pdf("/Users/magnusnygardosnes/Dropbox/10000_Lovers/Junk_used_for_exploratory/Temp/imp_exp_loc_USA.pdf", width = 10, height = 8)
plot_relative_fraction(implocexp_USA)

#dev.off()


#pdf("/Users/magnusnygardosnes/Dropbox/10000_Lovers/Junk_used_for_exploratory/Temp/imp_exp_loc_EUR.pdf", width = 10, height = 8)
plot_relative_fraction(implocexp_EUR)

#dev.off()

The absolute estimates on the same periods are shown below.